Draft Genome of a Type 4 Pilus Defective Myxococcus xanthus Strain,
Susanne Müller,aJonathan W. Willett,bSarah M. Bahr,aJodie C. Scott,cJanet M. Wilson,dCynthia L. Darnell,aHera C. Vlamakis,e
John R. Kirbya
Department of Microbiology, University of Iowa, Iowa City, Iowa, USAa; University of Chicago, Department of Biochemistry and Molecular Biology, Chicago, Ilinois, USAb;
The Forsyth Institute, Department of Microbiology, Cambridge, Massachusetts, USAc; Division of Select Agents and Toxins, Office of Public Health Preparedness and
Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USAd; Harvard Medical School, Department of Microbiology and Immunobiology, Boston,
S.M., J.W.W., and S.M.B. contributed equally to this work.
Myxococcus xanthus is a member of the Myxococcales order within the deltaproteobacterial subdivision. Here, we report the
Received 9 May 2013 Accepted 13 May 2013 Published 20 June 2013
Citation Müller S, Willett JW, Bahr SM, Scott JC, Wilson JM, Darnell CL, Vlamakis HC, Kirby JR. 2013. Draft genome of a type 4 pilus defective Myxococcus xanthus strain, DZF1.
Genome Announc. 1(3):e00392-13. doi:10.1128/genomeA.00392-13.
Copyright © 2013 Müller et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to John R. Kirby, firstname.lastname@example.org.
described in the late 19th century for their capacity to produce
macroscopic sporangioles or fruiting bodies (1). Organization
tion of two genetically distinct motility systems (2–29). Previ-
ously, the sequence of M. xanthus strain DK1622 was determined
(NC_008095.1) (30). Recently, we sequenced strain DZ2 (31).
These two laboratory strains are noted for behavioral differences
(2, 32, 33), and DZ2 has a larger genome (31).
M. xanthus DZF1 is directly descended from the intermediate
strain DK101, the progenitor for DK1622, and displays reduced
capacity for type IV pilus (T4P)-mediated motility. An earlier
study (34) mapped two point mutations in DK101 to pilQ, which
encodes the T4P secretin (G741S/N762G), accounting for some
have been noted, we sequenced DZF1 to determine if the addi-
relative to the progenitor.
M. xanthus DZF1 was sequenced at the University of Iowa
mosomal DNA was prepared as described previously (31) and
processed for sequencing following established protocols. The re-
sulting sequence comprises 388,477 reads totaling 249 Mb, repre-
75 contigs using Newbler software version 2.7. The resulting ge-
nome is approximately 9.28 Mb, similar to that for DZ2 (31), and
is approximately 147 kb larger than the DK1622 genome. The
RAST annotation server (35) predicts a total of 7,704 coding se-
quences (CDS) within the DZF1 genome.
The M. xanthus DZF1 sequence reveals a single nucleotide
yxococcus xanthus is a soil-dwelling deltaproteobacterium
with a genome length of ?9.2 Mb. The Myxococcales were
tution, but lacks the N762G substitution found in DK101 (34).
The impact of these SNPs has not been systematically determined
but affects the interpretation of several previous studies. Indeed,
deletion of mazF (encoding RNA interferase as part of a toxin-
antitoxin system) is synthetic with the pilQ allele in both DZF1
and DK101 to affect cell death (36, 37).
Current analysis is ongoing to determine the role of genes
found in DZF1, but not in DK1622, encoding proteins predicted
acid modification, and protein transport. Homologs to these
genes are found in DZ2 as well as other myxobacteria, including
Myxococcus fulvus, Stigmatella aurantiaca, and Sorangium cellulo-
sum. The presence of sequences unique to both DZF1 and DZ2,
while absent from DK1622, has been verified by PCR. Thus, the
differences between DK1622 and both DZ2 and DZF1 are attrib-
UV mutagenesis of DK101, which led to excision of one large
prophage (38, 39) and may have induced additional lesions. We
are investigating several unique sequences found in DZF1 and
DZ2 for their role in M. xanthus biology.
Nucleotide sequence accession number. This whole-genome
der the accession number AOBT00000000. The version described
in this paper is the first version.
Support for this work was provided by the University of Iowa and NSF
MCB-1244021 to J.R.K. Additional support for J.W.W. was provided by
NIH T32 GM077973.
We thank Tom Willett, Tom Bair, and Kevin Knudtson for helpful
discussions and data analysis.
Genome AnnouncementsMay/June 2013 Volume 1 Issue 3 e00392-13genomea.asm.org 1
Thecontentistheresponsibilityoftheauthorsanddoesnotrepresent Download full-text
the official views of NIH, NSF, or the University of Iowa.
Bot. Gaz. 17:389–406.
2. Berleman JE, Kirby JR. 2007. Multicellular development in Myxococcus
xanthus is stimulated by predator-prey interactions. J. Bacteriol. 189:
3. Blackhart BD, Zusman DR. 1985. “Frizzy” genes of Myxococcus xanthus
are involved in control of frequency of reversal of gliding motility. Proc.
Natl. Acad. Sci. U. S. A. 82:8767–8770.
4. Bulyha I, Schmidt C, Lenz P, Jakovljevic V, Höne A, Maier B, Hoppert
M, Søgaard-Andersen L. 2009. Regulation of the type IV pili molecular
machine by dynamic localization of two motor proteins. Mol. Microbiol.
5. Caberoy NB, Welch RD, Jakobsen JS, Slater SC, Garza AG. 2003. Global
mutational analysis of NtrC-like activators in Myxococcus xanthus: iden-
ment. J. Bacteriol. 185:6083–6094.
6. Campos JM, Zusman DR. 1975. Regulation of development in Myxococ-
cus xanthus: effect of 3=:5=-cyclic AMP, ADP, and nutrition. Proc. Natl.
Acad. Sci. U. S. A. 72:518–522.
7. Giglio KM, Caberoy N, Suen G, Kaiser D, Garza AG. 2011. A cascade of
coregulating enhancer binding proteins initiates and propagates a multi-
cellular developmental program. Proc. Natl. Acad. Sci. U. S. A. 108:
8. Huntley S, Hamann N, Wegener-Feldbrügge S, Treuner-Lange A, Kube
M, Reinhardt R, Klages S, Müller R, Ronning CM, Nierman WC,
Søgaard-Andersen L. 2011. Comparative genomic analysis of fruiting
body formation in Myxococcales. Mol. Biol. Evol. 28:1083–1097.
associated morphogen in Myxococcus xanthus. Proc. Natl. Acad. Sci.
U. S. A. 99:2032–2037.
gene expression in Myxococcus xanthus. Proc. Natl. Acad. Sci. U. S. A.
11. Kroos L, Hartzell P, Stephens K, Kaiser D. 1988. A link between cell
signaling during fruiting body development. Genes Dev. 2:1677–1685.
12. Kruse T, Lobedanz S, Berthelsen NM, Søgaard-Andersen L. 2001.
C-signal: a cell surface-associated morphogen that induces and co-
ordinates multicellular fruiting body morphogenesis and sporulation in
Myxococcus xanthus. Mol. Microbiol. 40:156–168.
13. Luciano J, Agrebi R, Le Gall AV, Wartel M, Fiegna F, Ducret A,
Brochier-Armanet C, Mignot T. 2011. Emergence and modular evolu-
tion of a novel motility machinery in bacteria. PLoS Genet. 7 e1002268.
14. MacNeil SD, Mouzeyan A, Hartzell PL. 1994. Genes required for both
15. Mauriello EM, Mignot T, Yang Z, Zusman DR. 2010. Gliding motility
revisited: how do the myxobacteria move without flagella? Microbiol.
Mol. Biol. Rev. 74:229–249.
16. Mignot T. 2007. The elusive engine in Myxococcus xanthus gliding motil-
ity. Cell. Mol. Life Sci. 64:2733–2745.
17. Mignot T, Kirby JR. 2008. Genetic circuitry controlling motility behav-
iors of Myxococcus xanthus. BioEssays 30:733–743.
18. Mignot T, Merlie JP, Jr, Zusman DR. 2005. Regulated pole-to-pole
oscillations of a bacterial gliding motility protein. Science 310:855–857.
19. Mignot T, Shaevitz JW, Hartzell PL, Zusman DR. 2007. Evidence that
focal adhesion complexes power bacterial gliding motility. Science 315:
20. Nudleman E, Wall D, Kaiser D. 2005. Cell-to-cell transfer of bacterial
outer membrane lipoproteins. Science 309:125–127.
21. Pathak DT, Wall D. 2012. Identification of the cglC, cglD, cglE, and cglF
genes and their role in cell contact-dependent gliding motility in Myxo-
coccus xanthus. J. Bacteriol. 194:1940–1949.
22. Shimkets LJ, Gill RE, Kaiser D. 1983. Developmental cell interactions in
Myxococcus xanthus and the spoC locus. Proc. Natl. Acad. Sci. U. S. A.
23. Singer M, Kaiser D. 1995. Ectopic production of guanosine penta- and
coccus xanthus. Genes Dev. 9:1633–1644.
24. Wei X, Pathak DT, Wall D. 2011. Heterologous protein transfer within
structured myxobacteria biofilms. Mol. Microbiol. 81:315–326.
25. Welch R, Kaiser D. 2001. Cell behavior in traveling wave patterns of
myxobacteria. Proc. Natl. Acad. Sci. U. S. A. 98:14907–14912.
26. Youderian P, Burke N, White DJ, Hartzell PL. 2003. Identification of
genes required for adventurous gliding motility in Myxococcus xanthus
with the transposable element mariner. Mol. Microbiol. 49:555–570.
27. Youderian P, Hartzell PL. 2006. Transposon insertions of Magellan-4
that impair social gliding motility in Myxococcus xanthus. Genetics 172:
28. Zhang Y, Ducret A, Shaevitz J, Mignot T. 2012. From individual cell
motility to collective behaviors: insights from a prokaryote, Myxococcus
xanthus. FEMS Microbiol. Rev. 36:149–164.
29. Zusman DR, Scott AE, Yang Z, Kirby JR. 2007. Chemosensory path-
ways, motility and development in Myxococcus xanthus. Nat. Rev. Micro-
30. Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA,
Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle
G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvarts-
beyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB, Kaplan HB.
2006. Evolution of sensory complexity recorded in a myxobacterial ge-
nome. Proc. Natl. Acad. Sci. U. S. A. 103:15200–15205.
31. Müller S, Willett JW, Bahr SM, Darnell CL, Hummels KR, Dong CK,
Vlamakis HC, Kirby JR. 2013. Draft genome sequence of Myxococcus xan-
32. Berleman JE, Chumley T, Cheung P, Kirby JR. 2006. Rippling is a
predatory behavior in Myxococcus xanthus. J. Bacteriol. 188:5888–5895.
33. O’Connor KA, Zusman DR. 1988. Reexamination of the role of autolysis
in the development of Myxococcus xanthus. J. Bacteriol. 170:4103–4112.
34. Wall D, Kolenbrander PE, Kaiser D. 1999. The Myxococcus xanthus pilQ
esis, social motility, and development. J. Bacteriol. 181:24–33.
35. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA,
Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson
R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T,
Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V,
Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using
subsystems technology. BMC Genomics 9:75.
36. Boynton TO, McMurry JL, Shimkets LJ. 2013. Characterization of
Myxococcus xanthus MazF and implications for a new point of regulation.
Mol. Microbiol. 87:1267–1276.
37. Lee B, Holkenbrink C, Treuner-Lange A, Higgs PI. 2012. Myxococcus
of developmental regulatory proteins and reexamination of the role of
MazF in developmental lysis. J. Bacteriol. 194:3058–3068.
38. Chen H, Keseler IM, Shimkets LJ. 1990. Genome size of Myxococcus
xanthus determined by pulsed-field gel electrophoresis. J. Bacteriol. 172:
39. Chen HW, Kuspa A, Keseler IM, Shimkets LJ. 1991. Physical map of the
Myxococcus xanthus chromosome. J. Bacteriol. 173:2109–2115.
Müller et al.
2 genomea.asm.org May/June 2013 Volume 1 Issue 3 e00392-13